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Detailed information for vg0809841368:

Variant ID: vg0809841368 (JBrowse)	Variation Type: INDEL
Chromosome: chr08	Position: 9841368
Reference Allele: CG	Alternative Allele: TG,C
Primary Allele: CG	Secondary Allele: TG

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TACTCGTCGGGGTGCATATTCCTATAGCCTGTCACCGATGACACTCATATGTGACGGGCTTGAAGTTAGGCCCGATTGAGATGACCTCCACTATCTCAAT[CG/TG,C]
GGCCCAAATACTGAGCCCGTCACAGATGAGTGTCATCGGTGACGGGCTCCAAAGAAGGCCCGATTGAGATGGCCTGAATGCCCGTCACCGATGACTCTTA

Reverse complement sequence

TAAGAGTCATCGGTGACGGGCATTCAGGCCATCTCAATCGGGCCTTCTTTGGAGCCCGTCACCGATGACACTCATCTGTGACGGGCTCAGTATTTGGGCC[CG/CA,G]
ATTGAGATAGTGGAGGTCATCTCAATCGGGCCTAACTTCAAGCCCGTCACATATGAGTGTCATCGGTGACAGGCTATAGGAATATGCACCCCGACGAGTA

Allele Frequencies:

Populations	Population Size	Frequency of CG(primary allele)	Frequency of TG(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	86.50%	0.00%	5.46%	7.96%	NA
All Indica	2759	98.80%	0.00%	1.05%	0.14%	NA
All Japonica	1512	62.20%	0.10%	14.35%	23.28%	NA
Aus	269	97.40%	0.00%	1.12%	1.49%	NA
Indica I	595	97.10%	0.00%	2.69%	0.17%	NA
Indica II	465	99.40%	0.00%	0.65%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	98.30%	0.00%	1.27%	0.38%	NA
Temperate Japonica	767	43.50%	0.10%	22.16%	34.16%	NA
Tropical Japonica	504	84.30%	0.20%	4.96%	10.52%	NA
Japonica Intermediate	241	75.50%	0.00%	9.13%	15.35%	NA
VI/Aromatic	96	89.60%	0.00%	2.08%	8.33%	NA
Intermediate	90	83.30%	0.00%	7.78%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0809841368	CG -> TG	LOC_Os08g16150.1	downstream_gene_variant ; 4337.0bp to feature; MODIFIER	silent_mutation	Average:52.45; most accessible tissue: Zhenshan97 flag leaf, score: 66.327	N	N	N	N
vg0809841368	CG -> TG	LOC_Os08g16140.1	intron_variant ; MODIFIER	silent_mutation	Average:52.45; most accessible tissue: Zhenshan97 flag leaf, score: 66.327	N	N	N	N
vg0809841368	CG -> C	LOC_Os08g16150.1	downstream_gene_variant ; 4336.0bp to feature; MODIFIER	N	Average:52.45; most accessible tissue: Zhenshan97 flag leaf, score: 66.327	N	N	N	N
vg0809841368	CG -> C	LOC_Os08g16140.1	intron_variant ; MODIFIER	N	Average:52.45; most accessible tissue: Zhenshan97 flag leaf, score: 66.327	N	N	N	N
vg0809841368	CG -> DEL	N	N	silent_mutation	Average:52.45; most accessible tissue: Zhenshan97 flag leaf, score: 66.327	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0809841368	1.32E-06	NA	mr1522	Jap_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251